User: ariel.balter

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ariel.balter140
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Posts by ariel.balter

<prev • 59 results • page 1 of 6 • next >
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Comment: C: Help defining contrasts in DESeq.
... The point is that we already have the data from the patients. The 0th order question is Case vs. Control. However, we also want to look at the effect of the genes in just the subgroup with the disease (Case). Just one of the many questions we want to ask. We have about a dozen genotypes to look at a ...
written 8 months ago by ariel.balter140
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Comment: C: Help defining contrasts in DESeq.
... @Kevin-- Sorry if I seemed too noob for you. I'm pretty well versed in reading manuals. I read the vignette section on contrasts many times. It shows how to pull out the log fold change for two levels of a given covariate. Not how to subset an entire covariate level. Google has not helped me either ...
written 8 months ago by ariel.balter140
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Help defining contrasts in DESeq.
... I'm working on a case/control study and including some other variables such as genotypes. One thing I want to do is a subgroup analysis of the genotypes for just the case group. The brute force method is to subset my data to the case group and run deseq on that. I'm very new to deseq and the very id ...
R contrasts deseq written 8 months ago by ariel.balter140
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Comment: C: BWA or STAR for microbiome 16s multiple sequence alignment?
... I hear ya. I thought it would be a more straightforward question. ...
written 13 months ago by ariel.balter140
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Comment: C: BWA or STAR for microbiome 16s multiple sequence alignment?
... I added a bunch of detail to the question. Maybe that will help. ...
written 13 months ago by ariel.balter140
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BWA or STAR for microbiome 16s multiple sequence alignment?
... I'm working with MISeq processed sequences of microbiome 16s samples. Is there any reason why I should use R tools like `msa` (Bioconductor) or `decipher` over NGS tools like `bwa` or `STAR`? Specifically, I'm using a [dada2](https://benjjneb.github.io/dada2/) workflow put out by the authors. My g ...
microbiome 16s alignment rna-seq written 13 months ago by ariel.balter140 • updated 13 months ago by Charles Warden7.4k
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Answer: A: Is there any way to install RStudio (or any other powerful IDE for R) without ro
... You can easily install both [rstudio](https://anaconda.org/r/rstudio) and [spyder](https://anaconda.org/anaconda/spyder) with conda without root access. You should also consider using Jupyter notebooks. You can install jupyter with conda as well. Caveats: 1) You need to install all the R packages ...
written 16 months ago by ariel.balter140
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Comment: C: samtools view by chromosome region chr:1000-1001000 creates "unknown reference n
... Yup! That did it. I thought I had tried that... Thanks! ...
written 2.5 years ago by ariel.balter140
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Comment: C: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi
... I don't see an equivalent to depth or bedcov in the [sambamba docs](http://lomereiter.github.io/sambamba/docs/sambamba-view.html) ...
written 2.5 years ago by ariel.balter140
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samtools view by chromosome region chr:1000-1001000 creates "unknown reference name" error
... I'm trying to create truncated versions of my bams for testing. The [samtools docs](http://www.htslib.org/doc/samtools.html) say: > REGIONS: > > Regions can be specified as: RNAME[:STARTPOS[-ENDPOS]] and all position coordinates are 1-based. > > Important note: when multipl ...
samtools written 2.5 years ago by ariel.balter140 • updated 2.5 years ago by Pierre Lindenbaum124k

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Great Question 10 months ago, created a question with more than 5,000 views. For Difference between samtools DEPTH and MPILEUP
Popular Question 13 months ago, created a question with more than 1,000 views. For How to use bedtools coverage
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Popular Question 16 months ago, created a question with more than 1,000 views. For Typical costs for RNA-Seq analysis
Popular Question 2.5 years ago, created a question with more than 1,000 views. For MACS2 with multiple replicates
Popular Question 2.5 years ago, created a question with more than 1,000 views. For MACS2 Narrow peak (narrowPeak) output format
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Difference between samtools DEPTH and MPILEUP
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Can't get samtools version: "unrecognized command"
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Relationship of bedGraph to wig.
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Typical costs for RNA-Seq analysis
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Tophat and Bowtie installed with Conda not working on test data.
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